Can we use the Agilent Bioanalyzer for PCR product evaluation instead of an agarose gel?

Yes, you can use the Agilent Bioanalyzer. We typically run a minimum of 96 samples therefore it is not cost-effective to use the Agilent Bioanalyzer for large number of samples. However, if you are testing a small number of samples (i.e. 16 samples), you may want to use it.